Saturday, February 25, 2017

First we got a bed of Atrichum angustatum. Int last photo u can almost make out the waves of micro spines across the leaves.

here they are begining to grow spore stalks.

this one has a more mature stalk. musta started growimg earlier. Or maybe this is A. altechristatum. I'll check.

Next there is Plagiomnium, not sure yet what species

Notice this species has a sprawling form of growth with leaves on either side of the stem and then a more upright growth form with leaves wrapped around the stem. This second growth form is the one with ovaries, gets fertilized and gives birth to the spore stalks. The spore stalks are actually separate moss individuals that dont grow leaves and dont have sex, just grow spores. The spores will grow into mosses with leaves ansd sex again and repeat the cycle. Why should moss live the same way we do?

these were also growing. I dont know what kind. I dont have my reference materials yet.

Wednesday, February 22, 2017

Complexity lab manual is a set of labs and exercises to learn to think about the origins of life from chemistry.
Could life have originated from chemistry alone, on Earth four billion years ago? There seems to be such a gap between the creativity and aliveness of all those flowers and fluttering birds on the one hand and the simplicity of rocks, water, and mud on the other hand. What does it mean to ask this question? Is there such a big gap between life and nonlife? IS life so complex and are rocks and mud so simple? What IS chemistry? What do we mean when we say life IS chemistry? What kind of question is it to ask how life came from chemistry alone? Alone from what?
The ultimate concrete way to get at this is to ask, can we start with a few bottles of purified nonliving chemicals and mix them together and create a living being from it? While we will explore this route to some extent, we should also ask: what would that have to do with how it started on Earth 4billion years ago? Did Earth start out as a few batches of simple chemicals?
What WAS Earth like when it was starting out 4.5 billion years ago? Was it a simple podge of a few kinds of chemicals that slowly got more complicated and became life?
The problem is... Possibly, there are NO simple places, EVER, in this universe!
The simplest place in the universe that we can conceive was way at the beginning, 14billion years ago when the universe blew up to a huge cloud of swirling Hydrogen gas with 14% Helium. Just as Jupiter's weather looks so complicated who knows what kinds of complicated swirls of these Hydrogen and Helium clouds there were... However... much of the complexity of Jupiter's weather is driven by heat flowing from the hot center to the cold outerspace, much as our weather is driven.
In the early universe it's not clear where there might have been heat flow? from what center?
Nevertheless drama soon unfolds! At first these clouds are all expanding apart. And there are minor fluctuations of density between them. There are ALWAYS random fluctuations. It seems that quantum mechanics gives us this. Random fluctuations are written into the laws of the universe! Counteracting the expansion is another aspect of the universe - gravity. This is pulling clouds together. At some point when the expansion dies down, gravity can begin to come into play and a random cloud of Hydrogen can start collapsing into its center. One might think that this cloud would collapse and collapse untill the Hydrogen is so compacted that it is a liquid, or even more compact than that. Also this compacting makes it hotter and hotter, think about what happens to your bicycle pump when you compress the air, it gets hot. Can this cloud get more and more compact and then perhaps simply wink out? The end?
Hardly! The physics of the universe apparently can never lead to dullness. If the cloud is more than even .08 times as massive as our sun is, it will get so hot when it compacts that the atoms of Hydrogen collide with each other with so much energy that they start transforming themselves into Helium atoms. So there ends up being a growing Helium core inside the star. Eventually enough of the Hydrogen gets used up and the star slowly cools off.
Unless it's BIGGER. If it's more than 3 times as massive as the sun... the Helium gets compacted hot enough and then starts joining up and transforming into Carbon, Nitrogen and Oxygen. Now THESE are interesting chemical elements.
Out between the stars, the most interesting thing hydrogen can do is join up in pairs, H2, and thats it. But these bigger stars, with their Carbon, Nitrogen and Oxygen... Once they form cores with those elements inside and use up enough of their Hydrogen and Helium, they start expanding into red giants, become unstable and start spewing off some of their new cooked elements into outerspace. As these gasses expand and cool, some of the atoms can combine and we get molecules. Water from the Hydrogen and Oxygen, H2O, methane from the Carbon and hydrogen CH4, ammonia from the Nitrogen and Hydrogen NH3, even a little Carbon dioxide CO2, even a little Cyanide HCN, even some carbons can collide with each other and ethane C2H6... the game is afoot.
That's a LITTLE bit of chemistry, but how about BIGGER stars? When they are more than 8 solar masses and there is enough gravity to create enough pressure and temperature to cook up many elements all the way up to silicaon and iron. There the cooking stops. Physics doesn't allow any more spontaneous combinations past Iron. Is THAT the end of the story? Hardly! If the cooking stops in such a massive star, the radiation streaming outward can no longer counteract the stupendous gravity pulling inward and the star quickly implodes into a supernova. VERY BUSY nuclear reactions taking place in there this time, and the upshot is that the atoms get cooked and cooked by flinging radiation so that all the elements in the periodic chart get made. And then the star comits suicide and has a MASSIVE explosion. Supernova!
All these new cooked gasses are exploded rapidly into the surrounding layers of gasses also seeded by the lighter stars with their Hydrogen, Oxygen, Carbon, and Nitrogen. The rapidly expanding supernova gasses cause shockwaves in the surrounding gasses and trigger more rounds of clouds to compress and start collapsing into even more new stars.
With some added features of course... The universe is never dull! Since there are so many more elements and compounds swirling aroud the stars now, as they contract and start forming they also form disks around themselvs and the gasses, and ice particles and dust from silicon and iron (rock) starts colliding into each other and PLANETS form.
Are planets just random mixtures of dozens of elements? Well, there are always processes..... The baby solar systems get sorted out. The star starts so hot at the begining that it blows away most of the volatile elements and compounds like Hydrogen, water vapour, methane etc... with its solar wind to the outer reaches of the surrounding disk. So a gradient forms in the infant solar system with high melting point rocks and metals close to the star and lower melting point ices and gasses further away. So planets close to the star tend to form more rocky, while planets further away tend to form with more ices and gasses.
That's the first sorting out that happens.
The second thing that happens is as the planetesimals are cobbling together bigger and bigger, the energy of their impacts and the gravitational force from their sizes cause more and more pressure and heat, till finally the higgledy piggledy minerals and rocks in them... some start melting, and the lowest melting point ones start first and the densist ones begin to sink to the bottom and the less dense ones float to the top. Each planet differentiates, like Earth with its Iron Nickle core, largely Olivine mantle (Iron and Manganese Silicate) and complex mix of lighter minerals floating atop in the crust.
Then there are the icy organic comets way in the outer reaches of the solar system. And in between are the gas giants like Jupiter. We are not yet sure whats in the center of that!
And then the pinball begins. Is the universe EVER simple? HELL NO! Newton showed us that when you solve the equations for gravity between two bodies you get 3 types of well defined orbits. If the bodies are not too incredibly fast, you get eternally stable circles or ellipses. If the bodies are fast enough they buzz past each other in parabolic arcs, never to see each other again. But add a just a THIRD body to the system? CHAOS. In fact we have not figured out all the possible solutions to even three bodies. And for a whole solar system of planets? We can tell by looking at the compositions of the asteroids in between Mars and Jupiter, that they look out of order. Some rocky ones outside and some icy ones inside. And we've recently learned to find solar systems around other stars. There are LOTS of possibilities.
It turns out that some time in our solar systems past, the orbits of the gas giants became a little unstable with this gravitational chaos and moved things around a bit. Flung asteroids higgledy piggledy at all the planets (meteorite impacts, craters!) and even fling the comets into the inner solar system. Either way, mixing icy bodies into the rocky planets and mixing rocky bodies into the icy planets...
We have to stop and notice something curious. We can have so many different kinds of complex planets because all these elements have curious mixes of properties!
Oxygen, Hydrogen, and Nitrogen atoms will bond with themselves, and form stable molecules of two each. These small molecules then form low melting point gasses and are found in the outer solar system. Hydrogen will combine with Oxygen and will form molecules in 3s, H2O, and this happens to be a rather sticky molecule so it has intermediate melting point and will form oceans which are found under the crusts of MANY solar system bodies, even on the surface of earth. Metal atoms bond with each other but not in twos or threes but in great masses that form crystals and form slightly higher melting point solids, that can however melt in the insides of planets and settle to the core because they are dense. Silicon and Oxygen will combine, not in twos or threes but not in great masses either, but in complicated rings, chains and networks and form a bewildering array of 100s of different minerals each with different properties and we find these in the mantles and crusts of planets. Carbon... well, we won't get into that yet, that's quite messy. That makes life.
The point about all this is... this is very unexpected! The atoms of each of these elements were simply cooked in the centers of stars by adding more and more protons together. Why are do the elements behave so DIFFERENTLY from each other? Why aren't atoms just BIGGER AND BIGGER AND BIGGER? WHY DIFFERENT?
One proton (and electron) by itself makes Hydrogen. Add another proton (and the universe seems to need to add in two neutrons too, to bind the protons together because they are positively charged and tend to repell each other... (why does the universe even FORM neutrons so this may happen?)) and you get Helium. Add another proton and you get Lithium, another and Berylium, another and Boron, then Carbon, then Nitrogen, then Oxygen... on and on up to 26 for Iron.
I've described the atoms getting cooked inside stars one proton at a time, but actually, the chemical behaviors are properties of the electrons that surround the protons in the nucleus, the center of the atoms. But only the nuclii of the atoms with the protons are formed in the centers of stars. The electrons get added to the nucleii later when the atoms and electrons are flung from the stars in explosions and then cool off. The important thing is that the number of electrons for each atom matches the number of protons. So, when an atom is made with 1 proton, it gets one electron: Hydrogen. When it gets made with 6 protons, it gets 6 electrons: Carbon. I'll ignore the neutrons and isotopes and radioactivity, isn't the universe complicated enough already?)
Why aren't the atoms just bigger and bigger versions of Hydrogen? Why do they behave SO differently? Berylium combines in great masses and makes a brittle metal. Boron with one more proton exhibits a sudden jump in behavior, it forms chains and rings and geodesic domes, but oddly is formed in very tiny amounts in stars.
Carbon with one more proton, forms these chains and rings but also forms very stable bonds with Oxygen and Hydrogen so that the forms CO2, CO3 (soluble in water) and CH4 form. The carbon compounds are much more stable too. Add one more proton and we get Nitrogen. Spends most of its time as N2, a gass because that bond is VERY stable, but some Nitrogen gets incorporated stably in carbon compounds. But nitrogen on its own does NOT form chains and rings like carbon does. Add one more proton and we get Oxygen. Oxygen also doesn't form chains and rings but simply diatomic O2 molecules so is a gas but much more reactive than N2. Oxygen combines with hydrogen to form a very reactive and sticky liquid, water. Add one more proton and we get fluorine and that's so reactive that the only stable forms it gets into are solid minerals like fluorite, CaF2. Add one more proton and we get Neon. A noble gas, no chemistry at all, not even Ne2, so it must get very cold to even liquify.
Add another proton and all of a sudden we get chemistry again, in fact... Sodium, which behaves like Lithium and the sequence starts again, each addition of a proton gives us an element that behaves subtly like the one above it in the periodic table, though not quite.
Aluminum is below Boron and ought to have similar properties but is much more stable in minerals and there's a 1000 times more of it in the universe. Silicon is below Boron and to the right, should be even more similar, but doesn't form the so many chains and rings by itself, only with oxygen. With oxygen it forms the vast assemblage of the most common mineral types. Silicon IS below Carbon, but that's not a match either. Carbon dioxide is a water soluble gas and silicon dioxide is quartz, a rock. There are just too many wild differences.
Why, why, why, is the universe at this most basic level so complicated? What's going on? Why isn't each atom just a bigger version of the previous one? Why do they have such peculiar distinct properties in combination with each other?
Well the quantum physics of all this is very complex, and while we have systems to help us explain what's going on, it isn't so easy to predict the properties from scratch. It has something to do with math.
Here are some clues.
Let's start with the simplest math imaginable, the counting numbers. Let's count.
let's start with:
1, add 1 and get
2, add 1 and get
3, add 1 and get
4 at this point lets notice some things. If we just mix in one more mathematical operation, multiplication we get some interesting patterns. 4 is a product of 2 and 2.
5 is not a product and so is called a prime number
6 that's a product of 2 and 3
7 another prime
8 that's a product of 2x2x2 hmm
9 that's a product of 3x3, already the pattern of prime, product, prime, product is broken
we can continue this and see more complication. I'll just list out the primes and show the gaps of numbers with products:
5 _ 7 _ _ _ 11 _ 13 _ _ _ 17 _ 19 _ _ _ 23 _ _ _ _ _ 29 _ 31
_ _ _ _ _ 37 _ _ _ 41 _ 43 _ _ _ 47 _ _ _ _ _ 53 _ _ _ _ _ 59
There's no pattern! it's impossible to predict what will happen next!
we can look at the pattern this way too:
3 no factors
4 2x2 two identical factors
5 no factors
6 2x3 two different factors
7 no factors
8 2x4 or 2x2x2 2 diff factors or 3 identical factors
9 3x3 two identical factors
10 2x5 two diff factors
11 no factors
12 2x2x3 3 factors two different
etc...
if we were arranging these into shapes, 4, 6,. 9, 10 could be made into squares and rectangles
8 can be made into a cube, requiring 3 dimensions...
The mathematics behind the properties that atoms get just by adding in more and more electrons is much different, but jumps in behavior occur for similar reasons.
So let's review: we started off with random swirls of Hydrogen clouds and gravity pulled them into stars. And then because of quantum physics the Hydrogen atoms could start combining into a bewildering variety of atoms. And then because of a combination of gravitational forces and the quantum phyisics, some of these stars could spew out their new cooked atoms or even explode them out and give birth to new star systems which could then form planets because some of these atoms could make rock and ice and gases.
And the planets differentiate into complex places because again the weird properties of these atoms interact with macroscopic physiscs and give different densities and melting and boiling points.
All because of math.
And planets become complex places. Even without life. A survey of half a dozen bodies in the solar system will be bewildering.
Dry barren rocky mercury. Venus with its sulfuric acid clouds with two different chemical regions that we have yet to explore in detail because, oh, yeah, it happens to be 885 degrees Fahrenheit and 90 times Earth atmospheric pressure. Robots don't work in that. Mars, dry and rocky with some Carbon dioxide ices and water ices, and chlorate surface. Pretty dead and oxidized but it WAS wet in the past and our marsrobots have found many different minerals.
The moons of the gas giants. Io with its sulfur volcanoes! Europa, Callisto, Ganymede, Enceladus with their frozen over oceans, though the oceans of Enceladus break through the ice every now and then and spurt guysers! And because we just happened to have recent;y flown our Cassini spacerobot THROUGH those guysers (she's already been flyin out there 18 years, what the hell, she can take it!) we have hints that the ocean is interacting chemically with the rock seabed below.
Titan, now there is a fun mix! frozen over ocean over rock ball but the atmosphere has a hydrological cycle of methane and ethane over the frozen over ocean lakes and rivers of liquid methane slowly wearing away the ice rocks into smooth pebbles. We took pictures! There may be interesting chemical cycles there.
the gas giants themselvs are huge swirly weather patterns of Hydrogen and methane and ammonia over a liquid hydrogen center... we don't know much about what happens deep inside. Spacerobot Juno is there now, peering deep inside for the first time.
And pluto. Our most recent discovery. Icy rock planet. Ice mountains, Nitrogen glaciers flowing into a half frozen nitrogen paste ocean and methane snow with organic gunk haze in a very tennuous atmosphere. Maybe even cryovolcanoes from an internal ammonia water ocean deep below? who knows?
The comets have interesting surfaces, icy dusty rock, that get heated and vaporized by the sun every time they swoop close. what chemistry happens there? Every now and then one hits a planet.
And Earth... even though Earth's geology has been heavily modified and complexified by nearly 4billion years of life swarming over the place, breathing and pissing all over the place... we can infer that many of her chemically complex environments predate life. Maybe up to a 1000 different minerals arranged in complex formations.
Even before the planets formed... by studying meteorites that have fallen to earth and studying the asteroids in space from which most of the meteorites most surely have been chipped off, we can gain a picture of the building blocks of the solar system before planetesimals began to form.
There are presolar particles. Between a micron and a millimeter in size. Diamonds, zircons, calcium carbide, graphite, various metal flecks.... These predate the solar system, were made inside all those spewing and exploding stars that gave birth to our solar system.
And then the meteorites themselves are made of a conglomeration of these presolar grains, and funny millimeter sized beads called chondrules. These are various kinds of minerals that appear to have already formed and then had become molten quickly and then cooled quickly before getting pasted together with the presolar grains and metal flecks sometimes with much organic matter as the paste... We haven't figured out where the chondrules come from or how they melted and formed.
complexity everywhere we look.
When we study all these environments in detail, and add in all the complex planetary chemistry, our question of how did life form at the begining from simple chemistry becomes modified. The chemistry was NEVER simple.
As we begin to explore some laboratory examples of simple chemical systems that can elaborate into complex patterns, we should keep this in mind. Also keep in mind that we've barely begun to understand chemistry, we've only been at it for 150 years. And chemistry on the other planets? How much have we dug into them? We've had 1000s of chemists studying chemistry on Earth, but we've only sent a couple dozen spacerobots to other planets and they haven't been exceedingly equipped with the best chemistry labs! And they've only been at it since the '70s. So much to learn!